Establishment of a Pedigreed Rainbow Trout Broodstock Using Recirculating Aquaculture Technology and Genotyping

Final Report
Lyndon Fish Hatcheries Inc
AIMAP-2012-CA01

Company Overview

Lyndon Fish Hatcheries is a privately owned company owned by Lynn Rieck. The company is in the primary business of breeding and selling of Rainbow Trout fingerlings and eggs to fish farms in Ontario and abroad. The main hatchery is located just north of New Dundee. There is a second site located on the west side of Manitoulin Island. Lyndon also recently expanded into heated recirculation systems having two systems located in New Dundee that are 89,000 gallons in growing volume. The hatchery in New Dundee is federally inspected by DFO and has a disease free status under the Fish Health Protection Regulations. This allows the export of live fish and eggs from this facility to other provinces and countries. The site on Manitoulin is used primarily to grow fingerlings for cage culture operations on Manitoulin Island and in Parry Sound. Due to the size of the hatchery, our openness to embrace new technology and ideas, and the close proximity to Guelph, researchers in both genetics and fish pathology from the University of Guelph have been working with the hatchery on several projects. We have also been working with Dr. Amber Garber at Huntsman Marine Science Centre in New Brunswick to aide in setting up a broodstock program. Currently a large proportion of live fish eggs purchased by farmers in Canada come from a hatchery in Washington State called Troutlodge. They are our largest competitor as a result of their size and ability to supply eggs through most of the year. The less than adequate performance of their fish and the desire by Canadian growers to buy domestic, however, is causing fish farmers to explore other options. Our commitment to deliver a quality product at the desired time along with an increase in our broodstock population has allowed us to compete on a small level with Troutlodge. With the aid of our scientific partners we plan to implement a selective breeding program that will give us that edge to compete and give Canadians growers not just another option, but a preferred domestic option when deciding where to purchase eggs and fingerlings.

Business Opportunity

With respect to animal breeding, aquaculture in Canada falls well behind terrestrial agriculture. The poultry industry is an example where significant gains in performance are made with every generation. Establishing breeding programs is often on a list of important issues in many aquaculture groups across Canada. In the past, the only way to establish a selective breeding program was to have a large number of individual tanks in order to grow fish to a size where a passive integrated transponder (PIT) tag could be injected so that information on parentage could be easily recovered if mixing fish into a production environment. For many fish hatcheries including our own, the cost of having dedicated tanks for this purpose is not economically feasible. Currently, with advancements in molecular genetics, genotyping the offspring will allow researchers to determine who the parents were without the overwhelming costs of individual family tanks. This project will also give meaningful data of performance in a production setting as opposed to lab results. Knowing that the facility that you purchase eggs from has a selective breeding program will also give additional credibility to our product. Many of our customers know that our fish already perform very well, but in today's marketplace, if you're not making advancements in performance or quality then you will fall behind. Our goal is to expand our export market and to do that we need to make a good product even better. The increase in sales alone will allow our hatchery to operate at its full potential and make our hatchery operation more profitable.

Project Details

Duration of Project

Technical Objectives

1. Genotype all broodstock individuals in the 2012/13 spawning cycle and all new broodstock in the 2013/14 spawning cycle.
   The genotyping efforts for these fish have been an ongoing task and efforts continue. The extended duration of the genotyping efforts are attributed to the significant number of samples to be processed.
2. Track crosses made and families or progeny lots produced.
   Progeny from crosses are continually monitored and weekly reports are generated to indicate average sizes for each lot of fish as well as temperature data to substantiate growth rates for each lot individually. The parents of the crosses are each identified in the spawning file, their PIT tag is recorded, and tissues samples from each parent are being genotyped. This provides the opportunity to ensure that genetic diversity is maintained and no cross breeding occurs in the future.
3. Continued development of QTL-specific multiplex groupings for future use in marker-assisted selection programs and pedigree analysis.
   There has been continued work on this objective and efforts continue. Markers to be selected for have been increased from 6 to 8, which enables genetic selection for growth, spawning time and maturity. As more progeny go through the AIMAP system, increasing research can be performed in this regard to further validate the growth markers.
4. Rear sub-sets of the 2013/14 progeny lots at the Alma Aquaculture Research Station (AARS)
   As of March 24, 2013 there have been 10 sub-sets of the AIMAP progeny lots which are also being reared at Alma for research. As of April 1, there are a total of 5,142 fish being reared at Alma.
5. Establishment of a formal breeding program for growth improvement in the Lyndon strain
   There has been numerous discussions regarding the development of a national breeding program, however at this time Lyndon is continuing to work towards the development of a formal program with the hope that government assistance will be available to offset the cost of this effort and facilitate the genetic growth potential of the Lyndon strain. Currently we are selecting for growth, and disease resistance with genetic analysis of the progeny to follow, once they reach 50 grams in size.

Plan of Work and Results

System Development

In January of 2012 initial design stages were put into the place for the design of the system from a genetic and structural standpoint. Various different researchers and designers were consulted to ensure that the system would be designed with all of the best available information available.

From January to April of 2012 the design and procedural mechanisms were put in place. By April the design phase was complete and construction was able to begin.

Equipment installation took place from mid-March until mid-September. Equipment installation encountered several delays as different structural changes needed to be made to the building to accommodate the plumbing for the system. In addition to structural modifications, different aspects of the design were able to be modified to improve the effectiveness of the system. All of the above factors contributed to equipment installation requiring more time than initially anticipated, however the end result was a system which would be more effective.

System Operation

The system was fully operational by mid-September, with the fish eggs to be introduced from eggs spawned on October 4, 2012, from this date onward crosses were created for this system virtually every week that spawning occurred. The parents for each family introduced into the system is tracked and archived in the broodstock database and tissue samples for the parents are sent to Guelph for further analysis which includes genotyping.

As of March 24, 2012 there are fish from 300 families being reared in the system taken 19 spawning days. These 19 groups range in size from sac fry, up to 13 grams in size.

Fish are hand fed a minimum of 3 times per day with oxygen, temperature, and ammonia levels are routinely monitored to ensure that environmental conditions do not adversely affect growth rates.

Upon reaching specified sizes, fish are also graded to select the fastest growing fish and every week, each lot that is large enough to be feeding is sampled to track growth rate variance between groups to identify if fish growth is impacted by the time of year that they were spawned.

Bacterial Coldwater Disease Resistance

Ongoing research with Dr. John Lumsden of the University of Guelph has shown that the Lyndon strain has varied resistance to Coldwater disease. In preliminary trials, morbidity after bacterial injection ranged from 9.5% to 85.7%. There has also been research which shows that disease resistance is positively linked to growth, this means that the fastest growing fish would also be the most resistant. With this significant range in resistance as well as supporting research, it was discovered that the AIMAP system presented an opportunity to screen for disease resistance as well as growth rates.

After consultation with Dr. Lumsden, it was decided that we would screen for disease resistance by rearing the fish in disease infected waters and withholding treatment to only allow the resistant fish to survive. The disease resistant fish would then continue to selected for growth for the remainder of their life cycle. In the AIMAP system, Coldwater disease was present in the water; therefore the fish were surrounded by the bacteria. To date it has been observed that approximately 55% of the fish have not been disease resistant; however, the resistant fish seem to be the largest fish.

This step has modified the grading process as fish populations are significantly reduced by eliminating the fish that are not resistant to the disease, and the selection process to select based on size has been modified slightly but the end result is selecting for growth as well as disease resistance. This was a very exciting development as this approach allows us to approach disease resistance from a genetic and phenotypic standpoint. The development of a strain that is resistant to Coldwater disease leads to a reduced dependence on antibiotics, which creates a product that is healthier for the consumer, and also allows the producer to reduce medication costs.

Future Progress

Family creation will continue and progeny will be transferred out of the AIMAP system upon reaching their final grading period. Upon reaching this stage they will be integrated into Lyndon's traditional facilities for future selection and integration into the Lyndon broodstock.

Genetic research efforts will continue in the development of Quantitative Trait Loci (QTL)-specific multiplex groupings for future use in marker-assisted selection programs and pedigree analysis. There are also efforts being devoted to the development of Polymerase Chain Reaction (PCR) testing methodology for disease resistance.

With the foundation of superior progeny generated by this system, there are significant economic and research possibilities which are now able to be pursued with greater knowledge and experience.

Challenges and Difficulties

There were some operational difficulties which were encountered. The original design of using screens to separate lots of fish needed to be altered as some small fish were able to slip through gaps between the screen and the wall of the tank, with some of the fish being under 0.5 grams, the smallest gap could result in mixing between lots. This issue was solved by designing and creating mesh “inserts” where the fish were reared in “baskets” which were made to be identical to the original design, except the inserts provided a complete mesh barrier and therefore prevented future issues from arising.

Project's Impact and Forecast

At the moment there are no other commercial rainbow trout breeding facilities in Canada that have a breeding program such as the one that Lyndon has been able to establish with the assistance of this project. This will put us on the road to competing on an international level with Troutlodge and other European egg suppliers. With a breeding program in place, our credibility as a hatchery will improve and this will add value to our broodstock and could lead to further investment from other firms. It is also important to note that presently Canadians rely heavily on eggs from outside of Canada. Borders have been known to be shut down due to disease issues. If this were to happen tomorrow, many Canadian businesses would be in peril. Having a domestic supply of disease free eggs is very good insurance against these situations.